|
| Status |
Public on Feb 24, 2020 |
| Title |
dcl4 sRNA |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence (stage 1-12) immature flower buds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Columbia
genotype/variation: dcl4-2
tissue: inflorescence (stage 1-12) immature flower buds
molecule subtype: small RNA
|
| Growth protocol |
Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Inflorescence small RNA was isolated with TRIzol reagent (Invitrogen) and concentrated using the mirVana microRNA Isolation Kit (Ambion).
For AGO1-IP samples, AGO1 was immunoprecipitated from inflorescence tissue using Agrisera anti-AGO1 primary antibody. RNA was isolated from AGO1-IP or mock-IP samples using TRIzol reagent.
Size-enriched small RNAs were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina).
Multiplexed libraries were sequenced on HiSeq2500 or HiSeq4000.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
total small RNA
|
| Data processing |
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
ShortStack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.
|
| |
|
| Submission date |
Nov 04, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
R. Keith Slotkin |
| E-mail(s) |
kslotkin@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 North Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE133618 |
Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes |
|
| Relations |
| BioSample |
SAMN13192921 |
| SRA |
SRX7099475 |
